A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies
Studying the antibody response to infection or vaccination is essential for developing more effective vaccines and therapeutics. Advances in high-throughput antibody sequencing technologies and immunoinformatic tools now allow the fast and comprehensive analysis of antibody repertoires at high resol...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Vaccines |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-393X/11/6/1099 |
| _version_ | 1797592467463208960 |
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| author | Kristel Ramirez Valdez Benjamin Nzau Daniel Dorey-Robinson Michael Jarman James Nyagwange John C. Schwartz Graham Freimanis Angela W. Steyn George M. Warimwe Liam J. Morrison William Mwangi Bryan Charleston Marie Bonnet-Di Placido John A. Hammond |
| author_facet | Kristel Ramirez Valdez Benjamin Nzau Daniel Dorey-Robinson Michael Jarman James Nyagwange John C. Schwartz Graham Freimanis Angela W. Steyn George M. Warimwe Liam J. Morrison William Mwangi Bryan Charleston Marie Bonnet-Di Placido John A. Hammond |
| author_sort | Kristel Ramirez Valdez |
| collection | DOAJ |
| description | Studying the antibody response to infection or vaccination is essential for developing more effective vaccines and therapeutics. Advances in high-throughput antibody sequencing technologies and immunoinformatic tools now allow the fast and comprehensive analysis of antibody repertoires at high resolution in any species. Here, we detail a flexible and customizable suite of methods from flow cytometry, single cell sorting, heavy and light chain amplification to antibody sequencing in cattle. These methods were used successfully, including adaptation to the 10x Genomics platform, to isolate native heavy–light chain pairs. When combined with the Ig-Sequence Multi-Species Annotation Tool, this suite represents a powerful toolkit for studying the cattle antibody response with high resolution and precision. Using three workflows, we processed 84, 96, and 8313 cattle B cells from which we sequenced 24, 31, and 4756 antibody heavy–light chain pairs, respectively. Each method has strengths and limitations in terms of the throughput, timeline, specialist equipment, and cost that are each discussed. Moreover, the principles outlined here can be applied to study antibody responses in other mammalian species. |
| first_indexed | 2024-03-11T01:51:26Z |
| format | Article |
| id | doaj.art-d8fce2573d704e94acaa56c761ca4797 |
| institution | Directory Open Access Journal |
| issn | 2076-393X |
| language | English |
| last_indexed | 2024-03-11T01:51:26Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Vaccines |
| spelling | doaj.art-d8fce2573d704e94acaa56c761ca47972023-11-18T12:59:12ZengMDPI AGVaccines2076-393X2023-06-01116109910.3390/vaccines11061099A Customizable Suite of Methods to Sequence and Annotate Cattle AntibodiesKristel Ramirez Valdez0Benjamin Nzau1Daniel Dorey-Robinson2Michael Jarman3James Nyagwange4John C. Schwartz5Graham Freimanis6Angela W. Steyn7George M. Warimwe8Liam J. Morrison9William Mwangi10Bryan Charleston11Marie Bonnet-Di Placido12John A. Hammond13The Pirbright Institute, Pirbright GU24 0NF, UKThe Pirbright Institute, Pirbright GU24 0NF, UKThe Pirbright Institute, Pirbright GU24 0NF, UKThe Pirbright Institute, Pirbright GU24 0NF, UKThe Pirbright Institute, Pirbright GU24 0NF, UKThe Pirbright Institute, Pirbright GU24 0NF, UKThe Pirbright Institute, Pirbright GU24 0NF, UKThe Pirbright Institute, Pirbright GU24 0NF, UKKEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, KenyaRoslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKThe Pirbright Institute, Pirbright GU24 0NF, UKThe Pirbright Institute, Pirbright GU24 0NF, UKThe Pirbright Institute, Pirbright GU24 0NF, UKThe Pirbright Institute, Pirbright GU24 0NF, UKStudying the antibody response to infection or vaccination is essential for developing more effective vaccines and therapeutics. Advances in high-throughput antibody sequencing technologies and immunoinformatic tools now allow the fast and comprehensive analysis of antibody repertoires at high resolution in any species. Here, we detail a flexible and customizable suite of methods from flow cytometry, single cell sorting, heavy and light chain amplification to antibody sequencing in cattle. These methods were used successfully, including adaptation to the 10x Genomics platform, to isolate native heavy–light chain pairs. When combined with the Ig-Sequence Multi-Species Annotation Tool, this suite represents a powerful toolkit for studying the cattle antibody response with high resolution and precision. Using three workflows, we processed 84, 96, and 8313 cattle B cells from which we sequenced 24, 31, and 4756 antibody heavy–light chain pairs, respectively. Each method has strengths and limitations in terms of the throughput, timeline, specialist equipment, and cost that are each discussed. Moreover, the principles outlined here can be applied to study antibody responses in other mammalian species.https://www.mdpi.com/2076-393X/11/6/1099antibody discoveryIgMAT10x Genomicsantibody sequencingantibody repertoire |
| spellingShingle | Kristel Ramirez Valdez Benjamin Nzau Daniel Dorey-Robinson Michael Jarman James Nyagwange John C. Schwartz Graham Freimanis Angela W. Steyn George M. Warimwe Liam J. Morrison William Mwangi Bryan Charleston Marie Bonnet-Di Placido John A. Hammond A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies Vaccines antibody discovery IgMAT 10x Genomics antibody sequencing antibody repertoire |
| title | A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies |
| title_full | A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies |
| title_fullStr | A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies |
| title_full_unstemmed | A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies |
| title_short | A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies |
| title_sort | customizable suite of methods to sequence and annotate cattle antibodies |
| topic | antibody discovery IgMAT 10x Genomics antibody sequencing antibody repertoire |
| url | https://www.mdpi.com/2076-393X/11/6/1099 |
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